I have a feeling that this is due to the defaults being used for the DataTables configuration, rather than direct initialisation with the configuration object. Are you able to update your initialisation to include, specifically the tableTools object, in the initialisation please? I would probably consider that best practice anyway (although this does look like it might be a bug / limitation in TableTools) since the editor instance is being used and set in the defaults, which could cause issues with any other tables that are also initialised.

The other thing to try would be to use a deep extend - i.e. $.extend( true, ... ) since the default is a shallow copy which might also be causing issues.